EZtrampo Instructions
EZtrampo analyzes mitochondrial protein-coding genes to study nucleotide composition across functional protein regions (transmembrane, mitochondrial matrix, inner mitochondrial space). It generates partitioned datasets suitable for phylogenetic analyses.
- Reads FASTA files for the 13 mitochondrial protein-coding genes
- Aligns sequences across species
- Splits proteins into three regions:
TM: transmembraneMA: mitochondrial matrixIM: inner mitochondrial space
- Calculates compositional statistics and codon usage
- Produces graphical summaries
- Generates NEXUS partition files by codon, gene, strand, and domain
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Upload FASTA files. Acceptable formats are:
.fasta, .fa, .fsa, .fas, .fna, .ffn, .faa, .frn - Each FASTA file must correspond to a single genetic marker and be named accordingly.
- Please ensure that:
- only FASTA files are uploaded;
- taxon names are consistent across genes;
- sequences contain valid nucleotides only ( IUPAC ambiguity codes allowed );
- internal gaps are absent (they will be removed if detected).
- Select the appropriate NCBI mitochondrial genetic code
- Choose the closest available model organism. Alternatively, users can provide a custom model by:
- Optionally, users can select a gene order reference from the dropdown menu.